Genes, Natural Selection, and Evolution

Lecture 1

• A gene is a unit of heredity, it carries information from one generation to the next.
• Genes functionally encode instructions to produce proteins or other functional molecules that influence an organism's traits.
• Natural selection is the process by which traits become more common in a population due to their impact on survival and reproduction.
• Genes are fundamental to natural selection because they carry the traits subject to evolutionary pressures.
• Evolution relies on variation in traits, competition for resources, and the ability of individuals to reproduce.
• Evolution involves changes in the frequency of genetic variants within a population over time.
• Mutation, competition, and selection drive evolution.
• Evolution does not need selection; random processes like genetic drift, natural disasters, and random mating can lead to evolutionary changes.
• The environment, including other genes and individuals, directly influences gene frequency by affecting survival and reproduction.
• Molecular evolution involves the fixation of mutations in a population over time.
• Purifying selection removes harmful mutations.
• Positive selection fixes beneficial mutations.
• Neutral evolution occurs when mutations have no effect on fitness and drift randomly.
• Evolution can operate on single nucleotides, entire genes, proteins, gene order/composition, and chromosome structure.
• A gene is a union of genomic sequences that encode a coherent set of potentially overlapping functional products, which can serve multiple functions.
• Evolution can occur rapidly or gradually.
• Evolution is not designed but reacts to the current environment due to random mutations.
• Evolution optimizes organisms for survival. It is full of trade-offs and compromises, with constantly changing targets.
• Evolution is ongoing, and species are at different points in their evolutionary journey.
• All life has evolved for the same amount of time; no species is more "evolved" than another.

Lecture 2

• A genome is the entire genetic complement of a cell or individual, containing all genetic material (DNA or RNA) of an organism.
• The genome is essential to species evolution.
• Purifying selection removes harmful mutations at the molecular level.
• Positive selection fixes beneficial mutations at the molecular level.
• Neutral evolution involves mutations having no fitness impact and drifting over time at the molecular level.
• Gene content evolution is driven by mutation, recombination, and gene gain or loss.
• Bacteria have high gene turnover, with significant gene gain and loss.
• Intracellular bacteria undergo genome reduction, losing genes whose functions are supplied by the host.
• Eukaryotes have large amounts of non-coding DNA (98-99% of the genome), including introns, repetitive DNA, and regulatory elements.
• Non-coding regions in eukaryotes play a key role in gene regulation and complex gene expression patterns.
• The C-value paradox describes that genome size does not correlate with organismal complexity, especially in eukaryotes.
• Function in genomics refers to expressed sequences, i.e coding genes, or sequences involved in regulating gene expression (e.g., non-coding RNAs).
• Evidence of gene expression, binding activity, and evolutionary conservation is required to understand which parts of the genome are functional.
• Functional genomics tools and techniques are essential for identifying functional elements, but predicting function directly from the genome continues to be difficult.
• Comparative genomics helps identify functional genes by studying homologues across species.
• Conserved human genes in other species, like mice, allow for functional inferences through gene comparisons (e.g., synteny and orthologues).

Lecture 3

• A gene tree shows the evolutionary relationships of specific genes.
• A gene tree tracks the divergence of genes from duplication events.
• A species tree illustrates the evolutionary history of entire species, based on speciation events.
• Gene trees track individual gene lineage, while species trees reflect broader evolutionary events at the species level.
• Gene and species trees do not always align because gene divergence can happen due to both speciation and gene duplication.
• Orthologues are genes in different species that evolved from a common ancestral gene via a speciation event.
• Orthologues serve the same function in different species.
• Paralogues are genes related by a gene duplication event within the same species.
• Paralogues evolve in parallel, potentially gaining new functions or specializations.
• Understanding orthology and paralogy helps determine if genetic similarities are due to shared ancestry or gene duplication.
• Gene duplications create gene copies which can evolve new functions, acting as "raw material" for evolutionary change.
• Neofunctionalization is the process where duplicated genes acquire new functions.
• Subfunctionalization is the process where duplicated genes divide the ancestral function between them.
• Whole genome duplications (WGD), like the 2R hypothesis, propose that vertebrates underwent two rounds of whole genome duplication.
• WGD can lead to increased genetic complexity and development of new functional pathways.
• WGD is significant in plants, which can tolerate polyploidy (having multiple sets of chromosomes), allowing for evolutionary flexibility.

Lecture 4

• Transposable elements (TEs) make up a significant portion of eukaryotic genomes.
• TEs contribute to genetic diversity by promoting variations in DNA through their ability to move within the genome.
• DNA and retrotransposons impact the size of genomes, with some species showing variations in genome size.
• DNA transposons move through a "cut-and-paste" mechanism.
• Transposase enzymes excise the element from one site and inserts it into another site.
• The cut and paste process occurs during DNA replication or repair.
• Neutral insertions do not significantly affect the phenotype and may remain dormant or cause no harm.
• Beneficial insertions confer an advantage, creating genetic diversity selected over time.
• Harmful insertions disrupt a functional gene or regulatory region.
• The Ds transposon in maize caused spotted kernels due to its insertion into the pigmentation gene.

Lecture 5

• LTR retrotransposons have long terminal repeats (LTRs) at both ends and include endogenous retroviruses (ERVs).
• LTR retrotransposons mobilize via reverse transcription, producing a cDNA copy of their RNA intermediate, integrated into the genome by integrase.
• Non-LTR retrotransposons include LINEs (Long Interspersed Nuclear Elements) and SINEs (Short Interspersed Nuclear Elements).
• LINEs are autonomous and produce proteins for their own transposition.
• SINEs are non-autonomous and rely on LINE machinery for mobilization.
• Retrotransposons use a "copy and paste" mechanism.
• The RNA of the retrotransposon is reverse transcribed into cDNA by reverse transcriptase.
• cDNA synthesis is initiated by a single-stranded nick in the genomic DNA, facilitated by a LINE-encoded nuclease.
• Retrotransposon insertions disrupt coding sequences, causing diseases.
• Retrotransposons can also act as regulatory elements, enhancing or suppressing nearby genes.
• Retrotransposons sequences may act as enhancers, splice sites, or transcription factor binding sites.
• The insertion of retrotransposons into the genome can lead to genomic instability, such as increased recombination and rearrangements.
• Evolution of the placenta in mammals involves the capture of retroviral genes that originated from endogenous retroviruses.
• A jockey-like retrotransposon insertion affects the development of dorsal and hind wings in butterflies.
• Retrotransposons contribute to immune system function by regulating immune genes, influencing immune responses like inflammation and infection defense.

Lecture 6

• Sexual reproduction provides advantages through recombination.
• Sexual production fosters genetic diversity which is vital for adaptation, even though costly.
• The X chromosome is large, carries many genes (about 800 in humans), and is hemizygous in males (one copy).
• In males, any recessive allele on the X chromosome is immediately expressed.
• Beneficial intelligence alleles may have been selected under sexual selection on the X chromosome.
• The Y chromosome, much smaller than the X, carries genes for testis determination and spermatogenesis.
• The Y chromosome is poorly conserved across species.
• Originally, the Y and X chromosomes were homologous autosomes.
• Suppression of recombination between the X and Y means mutations on the Y chromosome cannot be corrected by recombination.
• The accumulation of mutations on the Y chromosome is exacerbated by high mutation rates during spermatogenesis and genetic drift.
• The loss of the Y chromosome is possible, and some species have adopted alternative sex-determining systems.
• The Y chromosome's degradation is a consequence of the loss of recombination.
• Muller's ratchet accelerates degradation, where harmful mutations accumulate because the Y chromosome cannot repair itself.
• In species that lose the Y chromosome, alternative sex-determining mechanisms can evolve, like the recruitment of Sox9.

Lecture 7

• Microchromosomes are small chromosomes found in the genomes of birds, reptiles, and other species.
• Microchromosomes are chromosomes with centromeres, telomeres, and GC-rich DNA content.
• Microchromosomes are smaller than macrochromosomes and typically have a high GC content.
• They are gene-dense, which means they carry many genes per unit of DNA.
• Microchromosomes maintain high gene density and cluster together in the nucleus.
• Microchromosome clustering may optimize gene expression.
• Microchromosomes have evolved over a long period.
• Microchromosomes present in species such as birds and reptiles have remained conserved for hundreds of millions of years.
• In species like birds of prey, there's evidence of microchromosome fusion and rearrangement.
• Some species transition from microchromosomes to macrochromosomes.
• Microchromosomes represent an ancestral chromosomal state, with large-scale duplications leading to macrochromosomes.
• Unlike reptiles and birds, mammals have lost microchromosome retention.

Lecture 8

• RNA Sequencing (RNA-Seq) measures relative mRNA abundance by sequencing all the RNA in a sample and aligning it to a genome.
• RT-qPCR (Reverse Transcription Quantitative PCR) measures relative RNA levels using internal reference genes and primers specific to the gene of interest.
• Single-Molecule Fluorescence In Situ Hybridization (smFISH) directly counts individual mRNA molecules in cells, allowing absolute quantification.
• Transcriptional Bursting is when RNA polymerases rapidly produce many mRNA molecules followed by off periods where no transcription occurs.
• Through experiments such as smFISH and live-cell imaging transcriptional bursting has been confirmed.
• Intrinsic noise is variability in gene expression due to stochastic (random) processes within a single cell.
• Extrinsic noise is variability in gene expression due to external factors or conditions affecting the entire cell population.
• Cell size is a major contributor to RNA variability between cells.
• Cells maintain a constant concentration of mRNA molecules per cell through feedback mechanisms coordinating transcription and degradation rates with cell volume.

Lecture 9

• DNA methylation is the addition of a methyl group to cytosine bases, repressing gene expression by preventing transcription factors binding.
• DNA methylation is maintained during DNA replication by maintenance methyltransferases (DNMT1).
• Histone modifications change chromatin structure, either tightening it to repress gene expression or loosening it to promote gene activation.
• Epigenetic regulation of DNA methylation influences the development of queen vs worker bees.
• In reptiles, such as bearded dragons and turtles, temperature influences epigenetic modifications that determine sex.
• In cancer, abnormal DNA methylation patterns can lead to the silencing of tumor suppressor genes.
• Rett syndrome and microcephalic dwarfism are linked to mutations affecting DNA methyltransferases and histone methyltransferases.
• 5-Azacytidine demethylates and treats blood cancers like leukemia by inhibiting DNA methyltransferases.
• CRISPR/Cas9 fused with transcriptional regulators precisely modifies epigenetic marks.

Lecture 10

• Eukaryotic genes consist of exons (coding regions) and introns (non-coding regions).
• Exons are spliced together to form the final mRNA after introns are removed
• Cassette exons are either included or skipped in the mRNA, leading to variations in protein products.
• Only one of two exons is included in mutually exclusive exon splicing, leading to alternative protein isoforms with different functions.
• The spliceosome can use different splice sites at the beginning or end of exons when splicing, leading to variations in exon length and impacting protein function.
• Aberrant alternative splicing can lead to diseases, such as spinal muscular atrophy (SMA) when incorrect splicing of the SMN1 gene results in the loss of protein function.
• RNA sequencing (RNA-Seq) can study alternative splicing by mapping sequencing reads to specific exons.
• Techniques like RT-PCR and CRISPR/Cas13 can manipulate splicing events to provide insights into the regulatory mechanisms of alternative spicing.

Lecture 11

• The central dogma of molecular biology describes the process of genetic information flow from DNA to RNA to protein.
• The translation phase occurs when proteins are created from mRNA with help from ribosomes and tRNA.
• Translation occurs in three stages: initiation, elongation, and termination.
• The initiation phase involves forming the initiation complex and scanning for the start codon.
• During elongation, amino acids are added to the peptide chain at a rate of 3-10 amino acids per second.
• Termination occurs when a stop codon is reached, and the ribosome releases the newly formed protein.
• Viruses target key factors in cap-dependent translation, forcing the cell to switch to cap-independent translation.
• Viruses often have internal ribosome entry sites (IRES) in their RNA, allowing them to bypass the usual translation initiation mechanisms.
• Ribosome profiling is a technique that can be used to study translation.
• Ribosome profiling isolates RNA protected by ribosomes and sequencing it to identify which parts of the mRNA are being translated.